In The Jefferson Lies, David Barton writes (page 135) that “Other presidential actions of Jefferson include:”

Signing federal acts setting aside government lands so that missionaries might be assisted in “propagating the Gospel” among the Indians (1802, and again in 1803 and 1804)

Directing the secretary of war to give federal funds to a religious school established for Cherokees in Tennessee (1803)

Negotiating and signing a treaty with Kaskaskia Indians that directly funded Christian missionaries and provided federal funding to help erect a church building in which they might worship (1803)

Assuring a Christian school in the newly purchased Louisiana Territory that it would enjoy “the patronage of the government” (1804)

I have not checked the accuracy of all these claims, but I assume them to be true. However, Barton’s writing makes it seem like Jefferson did these things in support of spreading Christianity to the Indians. However, Thomas Fleming writes in The Louisiana Purchase (pages 147-148) about the treaty selling Louisiana to the United States:

One provision of the treaty required that the United States continue to observe Spain’s compacts with the Indians. This meant that a Roman Catholic priest would soon be on the federal payroll.

As a result, some of Jefferson’s support of Christianity among the Indians–a clear violation of his belief in the separation of church and state–may have been forced upon him by Spain’s treaties with the Indians that the United States inherited when it took over Louisiana.

David Barton’s assertion that Jefferson promoted Christianity among the Indians from a personal religious belief appears to be unfounded.

NOTE: I have not researched this topic extensively (which is why I was hesitant to question a “leading scholar” in this field). I merely ran across this information during my research on entirely different topics.